As we can see on the WikiProject Breakfast and WikiProject Hampshire pages, the WikiProject boxes conflict with Flow a bit, which is something that needs to be considered for a large rollout - lest we anger the masses. I imagine this has been thought about, but has there been any ideas as of yet?
I was thinking of making a mockup for my idea, which is that there would be a "box" at the top of the page, either filling the right side (above the eventual table of contents) or above Flow, assuming the user doesn't have enough room for the former. Each WikiProject would have a name, logo, and Class/Importance in said box. It would also be the container for notices (Refideas, for example), and the timeline of events (peer review, reaching good article status, etc.). All of this being editable via a VisualEditor-esque interface. I think this'd look much better and facilitate organization of WikiProjects and edit suggestions for articles, without causing as much friction in the conversion of Talk pages to Flow upon its release.
Perhaps there are other, better ideas already on the roadmap, but I haven't seen any and figured I'd see if anyone liked mine.